Targets’ report corresponding to the functions that annotate any original expression matrix (with gene symbols as ids in rows, and sample ids in columns) and expands the annotated matrix to include the average (or sum) values for the annotations (as new extra rows)
library(ggplot2)
library(heatmaply)
## Loading required package: plotly
##
## Attaching package: 'plotly'
## The following object is masked from 'package:ggplot2':
##
## last_plot
## The following object is masked from 'package:AnnotationDbi':
##
## select
## The following object is masked from 'package:IRanges':
##
## slice
## The following object is masked from 'package:S4Vectors':
##
## rename
## The following object is masked from 'package:stats':
##
## filter
## The following object is masked from 'package:graphics':
##
## layout
## Loading required package: viridis
## Loading required package: viridisLite
##
## ======================
## Welcome to heatmaply version 1.2.1
##
## Type citation('heatmaply') for how to cite the package.
## Type ?heatmaply for the main documentation.
##
## The github page is: https://github.com/talgalili/heatmaply/
## Please submit your suggestions and bug-reports at: https://github.com/talgalili/heatmaply/issues
## Or contact: <tal.galili@gmail.com>
## ======================
##
## Attaching package: 'heatmaply'
## The following object is masked from 'package:BiocGenerics':
##
## normalize
library(targets)
library(stats)
Data loaded from file data/mrna.csv
Samples in rows; Features in columns
## # A tibble: 150 x 201
## sample RTN2 NDRG2 CCDC113 FAM63A ACADS GMDS HLA.H SEMA4A ETS2 LIMD2 NME3 ZEB1 CDCP1 GIYD2 RTKN2 MANSC1
## <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 A0FJ 4.36 7.53 3.96 4.46 2.26 6.02 5.01 3.22 4.73 5.10 4.56 3.99 6.42 2.47 4.58 8.08
## 2 A13E 1.98 7.46 5.43 5.44 4.03 4.34 6.18 2.86 5.41 4.21 5.14 3.76 6.61 4.98 5.17 7.30
## 3 A0G0 1.73 8.08 2.23 5.54 2.63 6.36 6.04 5.95 5.65 3.30 4.45 3.85 6.41 3.20 4.24 7.99
## 4 A0SX 4.36 5.79 3.54 4.74 4.27 4.00 7.09 5.01 5.90 5.48 3.76 5.23 6.02 4.30 4.25 5.41
## 5 A143 2.45 7.16 4.69 4.81 2.44 7.03 5.94 5.90 6.64 5.51 4.24 3.54 7.09 5.71 3.96 8.49
## 6 A0DA 4.77 8.75 4.31 5.31 3.24 4.24 6.91 6.59 5.86 3.77 4.26 4.80 6.05 4.01 2.07 5.90
## 7 A0B3 3.35 5.10 0.593 5.22 3.89 5.92 8.04 6.53 6.31 4.11 4.79 4.26 7.27 4.64 3.53 5.03
## 8 A0I2 1.81 3.79 2.72 4.36 4.20 4.83 9.13 4.98 5.30 5.15 5.76 2.46 3.79 6.90 1.91 6.39
## 9 A0RT 2.09 6.33 2.36 4.04 4.13 4.29 7.59 5.94 6.57 7.07 5.13 5.55 3.85 5.66 4.27 3.71
## 10 A131 4.34 4.70 3.64 4.03 3.14 5.25 6.35 6.06 6.32 4.89 5.73 4.52 6.57 5.42 3.36 5.74
## # ... with 140 more rows, and 184 more variables: TAGLN <dbl>, IFIT3 <dbl>, ARL4C <dbl>, HTRA1 <dbl>,
## # KIF13B <dbl>, CPPED1 <dbl>, SKAP2 <dbl>, ASPM <dbl>, KDM4B <dbl>, TBXAS1 <dbl>, MT1X <dbl>, MED13L <dbl>,
## # SNORA8 <dbl>, RGS1 <dbl>, CBX6 <dbl>, WWC2 <dbl>, TNFRSF12A <dbl>, ZNF552 <dbl>, MAPRE2 <dbl>,
## # SEMA5A <dbl>, STAT5A <dbl>, FLI1 <dbl>, COL15A1 <dbl>, C7orf55 <dbl>, ASF1B <dbl>, FUT8 <dbl>,
## # LASS4 <dbl>, SQLE <dbl>, GPC4 <dbl>, AKAP12 <dbl>, AGL <dbl>, ADAMTS4 <dbl>, EPHB3 <dbl>, MAP3K1 <dbl>,
## # PRNP <dbl>, PROM2 <dbl>, SLCO3A1 <dbl>, SNHG1 <dbl>, PRKCDBP <dbl>, MXI1 <dbl>, CSF1R <dbl>, TANC2 <dbl>,
## # SLC19A2 <dbl>, RHOU <dbl>, C4orf34 <dbl>, LRIG1 <dbl>, DOCK8 <dbl>, BOC <dbl>, C11orf52 <dbl>,
## # S100A16 <dbl>, NRARP <dbl>, TTC23 <dbl>, TBC1D4 <dbl>, DEPDC6 <dbl>, ILDR1 <dbl>, SDC1 <dbl>, STC2 <dbl>,
## # DTWD2 <dbl>, TCF4 <dbl>, ITPR2 <dbl>, DPYD <dbl>, NME1 <dbl>, EGLN3 <dbl>, CD302 <dbl>, AHR <dbl>,
## # LAPTM4B <dbl>, OCLN <dbl>, HIST1H2BK <dbl>, HDAC11 <dbl>, C18orf1 <dbl>, C6orf192 <dbl>, AMPD3 <dbl>,
## # COL6A1 <dbl>, RAB3IL1 <dbl>, APBB1IP <dbl>, PSIP1 <dbl>, EIF2AK2 <dbl>, CSRP2 <dbl>, EIF4EBP3 <dbl>,
## # LYN <dbl>, WDR76 <dbl>, SAMD9L <dbl>, ASPH <dbl>, RBL1 <dbl>, SLC43A3 <dbl>, HN1 <dbl>, TTC39A <dbl>,
## # MTL5 <dbl>, NES <dbl>, APOD <dbl>, RIN3 <dbl>, ALCAM <dbl>, C1orf38 <dbl>, PLCD3 <dbl>, BSPRY <dbl>,
## # NTN4 <dbl>, IL1R1 <dbl>, EMP3 <dbl>, ZKSCAN1 <dbl>, FMNL2 <dbl>, ...
Features in ROWS: 200
Samples in COLUMNS: 150
(Showing only partial output)
tar_read(dframe)[1:10,1:10]
## A0FJ A13E A0G0 A0SX A143 A0DA A0B3 A0I2 A0RT A131
## RTN2 4.362183 1.984492 1.727323 4.363996 2.447562 4.770798 3.3520618 1.810382 2.094460 4.340912
## NDRG2 7.533461 7.455194 8.079968 5.793750 7.158993 8.748061 5.0984040 3.791965 6.327973 4.699950
## CCDC113 3.956124 5.427623 2.227300 3.544866 4.691256 4.305401 0.5932056 2.719169 2.357933 3.639056
## FAM63A 4.457170 5.440957 5.543480 4.737114 4.808728 5.307480 5.2175851 4.355919 4.041661 4.030187
## ACADS 2.256817 4.028813 2.629855 4.269101 2.442135 3.239909 3.8851534 4.200249 4.126817 3.135697
## GMDS 6.017940 4.341692 6.363030 4.001104 7.029723 4.236539 5.9178858 4.830286 4.292798 5.251649
## HLA.H 5.006907 6.178668 6.039563 7.087633 5.936138 6.909727 8.0433411 9.130370 7.591606 6.349572
## SEMA4A 3.217812 2.864659 5.946028 5.007565 5.901459 6.591109 6.5328925 4.982386 5.941057 6.055191
## ETS2 4.734446 5.411029 5.651670 5.902449 6.641225 5.858016 6.3091167 5.304488 6.571389 6.317800
## LIMD2 5.099598 4.211397 3.304513 5.479451 5.508654 3.766283 4.1138727 5.149344 7.071896 4.885183
Features in ROWS; Samples in COLUMNS
(Showing only partial output)
heatmap(data.matrix(dframe[1:40, 1:16]),
cexRow = 0.7, cexCol = 1,
Colv = NA)
Gene Ontology used: None. Annotations loaded from file: data/annotations.csv
Min. number of genes required to pass the filter: NA
Annotated categories: 5
tar_read(categ_sums)
## Neurogenesis Differentiation Developmental.protein Immunoglobulin.domain TF.complex
## 10 13 15 11 7
Features in ROWS: 200
Samples+Categs in COLUMNS: 155
(Showing only partial output)
head(tar_read(annot_matrix))
## A0FJ A13E A0G0 A0SX A143 A0DA A0B3 A0I2 A0RT A131 A124
## RTN2 4.362183 1.984492 1.727323 4.363996 2.447562 4.770798 3.3520618 1.810382 2.094460 4.340912 1.206280
## NDRG2 7.533461 7.455194 8.079968 5.793750 7.158993 8.748061 5.0984040 3.791965 6.327973 4.699950 8.676364
## CCDC113 3.956124 5.427623 2.227300 3.544866 4.691256 4.305401 0.5932056 2.719169 2.357933 3.639056 3.753526
## FAM63A 4.457170 5.440957 5.543480 4.737114 4.808728 5.307480 5.2175851 4.355919 4.041661 4.030187 5.193696
## ACADS 2.256817 4.028813 2.629855 4.269101 2.442135 3.239909 3.8851534 4.200249 4.126817 3.135697 2.789757
## GMDS 6.017940 4.341692 6.363030 4.001104 7.029723 4.236539 5.9178858 4.830286 4.292798 5.251649 5.610192
## A1B6 A1AZ A0YM A04P A04T A0AT A0AL A0CE A07R A0FL A150
## RTN2 2.846980 1.222353 1.892681 2.293955 1.090914 2.534021 2.4179929 1.763550 3.280434 6.142850 2.308591
## NDRG2 7.790635 4.730645 6.332405 7.827413 7.436516 6.961400 8.8336442 6.544614 6.875960 10.260165 5.887077
## CCDC113 3.060775 4.506151 3.208926 1.881223 3.664815 3.319350 0.2849741 4.309775 2.222412 1.441558 3.790442
## FAM63A 3.819955 4.464141 4.559118 3.709155 5.139812 3.491093 4.6556456 5.179804 5.368074 5.961550 4.274774
## ACADS 4.125045 3.028432 3.393146 2.456713 2.409692 1.834359 4.2644283 3.688115 3.009596 3.850541 3.018863
## GMDS 5.601640 4.144106 4.708556 6.716958 5.173432 5.728591 5.7582700 5.420492 4.877815 6.642912 5.163194
## A0E0 A0U4 A0XU A0AV A0AR A0RX A0D2 A0CM A0WX A0T0 A0T2
## RTN2 0.6743217 2.218695 3.320557 3.690360 2.910988 2.179577 1.965177 1.903714 3.070428 2.360129 3.620557
## NDRG2 4.5619890 7.385044 7.341238 5.753302 9.515500 7.047445 6.725903 4.983993 6.789360 9.155272 7.013197
## CCDC113 2.2716035 4.860181 4.620859 2.898493 2.883201 3.553867 1.249060 1.779161 4.790587 4.160914 3.172523
## FAM63A 6.0971133 3.800083 4.955763 5.765022 4.940644 4.360755 3.873571 4.664145 4.569566 4.872187 4.834117
## ACADS 4.3603055 3.454774 2.629412 2.778064 4.266805 3.867138 2.698221 1.556919 3.506256 2.350685 4.589873
## GMDS 4.4246369 5.455150 5.699021 4.910252 7.105627 4.995109 5.584181 4.981640 4.736113 4.825226 5.816029
## A04U A0JL A147 A0B9 A1AI A14X A12V A1AY A0D0 A0SK A128
## RTN2 1.384660 3.243859 3.505726 2.650759 0.3327526 3.628534 2.813715 3.497809 1.949481 4.794359 1.957013
## NDRG2 8.911393 9.339442 7.000853 7.243034 7.5131668 8.894409 8.556629 5.543856 4.910012 4.484965 3.858092
## CCDC113 1.412959 3.440030 3.978750 3.947715 4.1002872 2.966176 2.243080 4.186226 3.734065 3.500417 4.236216
## FAM63A 3.002935 4.850530 5.789872 4.526164 4.4563209 6.017519 4.719815 5.140818 2.203462 4.008493 1.840127
## ACADS 4.236686 3.006019 2.561543 3.478710 2.1922975 3.740005 3.446792 3.021059 3.308981 3.099769 3.204864
## GMDS 4.715617 5.033427 3.392365 4.530231 5.4230176 6.103145 4.414810 5.021890 4.402124 3.941773 5.958135
## A04D A0A7 A094 A12L A0I9 A0EE A135 A152 A18P A18R A08X
## RTN2 3.264143 3.630609 3.838779 2.836670 4.724076 0.6962941 1.819296 1.986657 3.475001 4.354183 3.733788
## NDRG2 9.645246 5.026081 5.260215 3.344884 4.503244 5.8202163 5.403551 4.999541 4.823776 6.402254 4.675284
## CCDC113 3.930012 2.450502 1.773722 5.404862 4.622169 3.1173445 4.118666 3.577636 4.374714 3.983280 3.294215
## FAM63A 5.762041 3.948055 3.928293 5.957079 5.570075 3.9983956 4.021509 5.645919 5.640225 4.190554 3.351270
## ACADS 3.045266 3.193824 4.305221 3.095219 4.583606 3.0785379 2.832452 2.867549 3.070213 5.606610 3.359589
## GMDS 5.038067 4.443301 5.812546 5.134322 4.819258 6.7714094 3.013772 3.917772 3.582233 2.518043 4.138523
## A0TX A09X A1AT A12Q A12T A0RH A07I A04W A12P A0EQ A0D1
## RTN2 2.931286 1.973935 4.178227 2.454749 3.360365 3.105367 3.843009 2.413193 4.780633 2.043937 2.8101153
## NDRG2 6.297263 4.741524 4.883940 4.679603 3.993496 4.467796 3.360024 5.915364 3.728883 4.451327 5.8398955
## CCDC113 4.381832 1.385884 4.041319 5.460908 4.168762 3.280249 5.273710 4.304850 3.611869 3.922623 3.8977020
## FAM63A 4.210461 2.777252 5.143692 7.478075 4.102186 5.490180 6.218413 4.735519 5.428217 3.733726 4.5425832
## ACADS 3.222013 2.480992 2.690258 3.902902 3.739438 3.791578 1.207714 2.316943 4.292261 2.387349 0.8715574
## GMDS 4.649420 4.547114 4.445286 5.259775 4.632893 4.769685 5.248546 5.203775 2.470152 3.986822 6.0863133
## A09G A1B0 A14P A0T1 A137 A13Z A08L A0IK A12D A0XN A0B0
## RTN2 4.336523 2.460993 2.725320 3.987558 3.3557342 3.858600 3.683918 3.805449 4.913829 3.854908 2.937087
## NDRG2 5.890453 3.328238 4.519024 5.339332 4.1665630 5.779159 6.035885 5.045742 5.362417 4.280310 6.399544
## CCDC113 3.385647 5.015205 7.685072 4.294984 3.7349053 2.925652 4.962329 3.799215 4.361665 3.073338 3.187451
## FAM63A 4.905487 4.009917 3.683882 3.896515 4.7856232 4.552264 5.417161 4.361230 4.103027 4.575127 6.084497
## ACADS 3.521845 3.758492 3.220628 3.483945 0.9475664 1.905945 2.902085 2.096262 2.865018 2.541062 4.087720
## GMDS 5.095428 5.425335 5.134124 5.515992 4.2281563 6.193263 5.167644 6.601120 5.207890 3.069358 3.896811
## A18S A0CS A0EI A0IO A0T6 A1AU A07Z A0XS A1BD A08T A12Y
## RTN2 4.885975 4.812521 4.145511 4.770780 3.686174 4.234722 4.668950 5.163421 5.862224 4.492575 3.451556
## NDRG2 5.190614 5.481586 4.209690 4.894866 5.714241 6.655277 5.074468 5.716168 6.367080 5.924680 4.315363
## CCDC113 5.981202 4.514267 4.871415 4.923091 3.999832 4.978289 4.836763 3.099718 4.402046 3.565575 3.035121
## FAM63A 6.839739 5.960769 5.562853 5.903991 5.543870 5.967937 7.315990 5.370638 7.073223 6.133809 6.137805
## ACADS 3.807709 5.826708 3.213199 4.201494 3.211621 4.088356 6.577862 4.426710 4.262734 4.193605 3.455379
## GMDS 4.467859 4.661853 3.977644 4.568149 3.908653 3.413226 3.640991 3.483881 2.866784 5.025717 5.219259
## A0J5 A18F A0AS A0DV A140 A0SU A12A A0RM A0AZ A0EW A0XW
## RTN2 3.324178 3.699449 3.147610 4.551102 3.371083 5.279948 4.599786 4.961715 4.395032 3.669192 4.060707
## NDRG2 5.204543 6.743026 3.310945 6.751697 4.767956 6.742996 6.767056 7.121645 6.166074 7.481286 3.993213
## CCDC113 3.658085 3.213309 3.392015 3.561305 4.266360 4.197921 3.613720 2.031879 4.705795 3.912063 3.859653
## FAM63A 6.019478 6.467441 3.583159 5.693453 7.680580 5.517610 6.374306 6.552616 5.685660 5.385438 5.234679
## ACADS 4.348268 3.839791 2.573175 4.361170 4.958535 3.757448 3.926513 5.375324 3.461114 4.981446 2.939582
## GMDS 2.901918 3.613409 4.553301 4.581463 2.306479 3.604445 4.316497 3.573679 3.908730 4.028187 4.368607
## A12B A0BP A0RG A0T7 A08A A0DK A0SH A18N A06P A15L A0YL
## RTN2 4.955273 3.946813 5.161843 3.628120 5.319757 4.229001 4.549374 5.160065 4.418414 3.003667 4.394415
## NDRG2 6.554334 6.110317 5.282558 7.041361 5.670118 6.234561 5.734280 5.743608 5.550527 5.638583 7.329557
## CCDC113 3.729381 3.599571 3.652475 4.567336 4.213460 2.876254 3.266107 3.799948 3.408737 3.767432 4.225351
## FAM63A 7.175329 5.866863 6.740858 4.849512 6.421754 6.278993 4.586105 6.548107 6.284064 5.833073 5.909271
## ACADS 3.771734 4.873476 3.834633 5.031143 6.435726 3.401421 3.781805 5.203101 4.189855 1.428122 4.124782
## GMDS 4.924317 3.476359 4.232467 3.994755 4.211985 4.533902 4.445566 3.016115 4.291386 4.561102 4.448572
## A1AL A133 A086 A0I8 A0EA A09A A0DS A1B1 A0X0 A1AP A0W5
## RTN2 4.318402 4.567727 3.380619 3.591457 3.934620 3.534916 5.337452 3.156414 4.318445 4.434544 4.053462
## NDRG2 7.671057 5.631257 5.348448 6.711921 6.485034 5.598355 5.431434 6.889978 5.134913 4.996163 6.324229
## CCDC113 4.058701 4.856185 2.812439 4.245995 4.373684 4.435664 3.569027 4.403957 4.249242 3.360406 4.206724
## FAM63A 6.332046 6.715817 5.614007 6.305527 6.607800 6.053269 6.544494 4.557049 6.261542 7.132167 5.686577
## ACADS 3.830086 3.637716 3.446198 3.597418 5.298255 3.821643 3.157999 3.427855 4.405081 2.979350 3.717058
## GMDS 3.988674 4.967355 3.844804 3.978552 3.381281 4.133674 3.789697 4.472276 4.407352 3.292519 4.446478
## A0JF A1AV A0RO A08Z A0RV A0DP A0EX A15R A0FD A0ES A0BM
## RTN2 4.255694 4.976229 3.593910 3.338102 4.312011 4.391099 4.971500 5.829543 5.114808 4.491791 3.854894
## NDRG2 6.107624 4.682798 6.831737 4.578062 6.562096 6.629841 6.442082 6.122818 5.004968 7.224767 7.563725
## CCDC113 3.566409 5.538055 5.843992 4.027111 3.146601 4.792597 3.858766 4.058642 4.246867 4.211227 3.714711
## FAM63A 5.823695 6.984005 5.434283 5.675758 6.527390 6.071293 5.216955 6.802337 5.049330 5.603656 4.972501
## ACADS 4.724552 5.848000 1.918908 3.367570 3.087441 4.333238 3.814054 3.339114 3.457678 3.962619 4.167155
## GMDS 4.618498 5.651612 4.426422 5.717837 4.689314 4.153339 4.377855 2.615647 3.599680 4.249810 4.587572
## A0EU A12X A146 A0CD A0BQ A04A A0CT A0TZ A03L A1AK A0E1
## RTN2 2.760552 3.285527 2.181406 4.831567 4.930042 3.897918 5.226293 1.560674 3.682643 4.174028 3.240652
## NDRG2 4.972966 6.049840 5.570016 4.273907 6.153962 4.727599 6.574909 4.528818 4.927297 6.933249 6.032330
## CCDC113 3.250293 5.094973 4.711167 3.816242 4.304354 3.633439 1.783738 3.897716 4.111116 4.353695 3.004524
## FAM63A 5.821183 6.752349 6.352394 5.779353 6.357639 6.226870 5.881396 5.792156 4.983386 6.927104 6.454520
## ACADS 4.197412 4.716806 2.759397 5.127855 3.385413 1.853465 3.108414 3.464086 2.941760 4.921953 4.474807
## GMDS 3.129062 4.634938 3.824802 5.385437 4.917877 3.285392 1.983430 2.888763 4.328807 2.646618 5.919961
## A0H7 A0FS A0BS A08O A12H A15E A0W4 Neurogenesis Differentiation
## RTN2 4.286326 4.728350 3.139900 4.346977 3.287485 4.684112 4.294419 0 0
## NDRG2 6.206116 6.857311 6.222359 5.708690 5.043387 6.274357 5.236494 1 1
## CCDC113 3.897574 3.088589 4.306467 3.995944 3.665758 4.599318 4.310629 0 0
## FAM63A 5.390505 6.047637 6.912236 6.189790 5.943128 5.335620 5.955053 0 0
## ACADS 1.802260 5.754979 5.317992 4.488860 4.823124 4.247261 4.631673 0 0
## GMDS 3.603636 3.581223 4.686750 3.186237 5.077987 3.627571 4.648448 0 0
## Developmental.protein Immunoglobulin.domain TF.complex
## RTN2 0 0 0
## NDRG2 1 0 0
## CCDC113 0 0 0
## FAM63A 0 0 0
## ACADS 0 0 0
## GMDS 0 0 0
Gene Ontology used: None. Annotations loaded from file: data/annotations.csv
Min. number of genes applied to filter: NA
Annotated categories: 5
Features+Categs in ROWS: 205
Samples in COLUMNS: 150
(Showing only partial output)
tail(tar_read(expd_matrix), ncol(categ_matrix))[,1:10]
## A0FJ A13E A0G0 A0SX A143 A0DA A0B3 A0I2 A0RT
## Neurogenesis 5.854374 5.556609 5.969148 5.948997 5.877565 6.268727 5.915049 4.614858 6.128434
## Differentiation 6.014111 5.693370 5.697298 5.963823 5.975038 5.968228 5.715979 4.721639 5.928967
## Developmental.protein 5.930771 6.054442 5.965397 6.027754 6.133427 6.201191 5.809003 5.059396 5.897052
## Immunoglobulin.domain 5.178721 4.594623 4.630296 5.565021 4.656773 4.682233 4.948528 4.624139 5.869650
## TF.complex 5.980126 5.808850 5.752035 6.298740 5.617033 5.528551 5.171721 4.449912 6.039300
## A131
## Neurogenesis 5.823166
## Differentiation 6.038837
## Developmental.protein 6.024545
## Immunoglobulin.domain 5.379455
## TF.complex 5.014576
Features+Categs in ROWS; Samples in COLUMNS
(Showing full and partial output)
p <- heatmaply(expd_matrix,
#dendrogram = "row",
xlab = "", ylab = "",
main = "",
scale = "none",
margins = c(60,100,40,20),
#grid_color = "white",
#grid_width = 0,
titleX = FALSE,
hide_colorbar = TRUE,
branches_lwd = 0.1,
label_names = c("Feature", "Sample", "Value"),
fontsize_row = 5, fontsize_col = 5,
labCol = colnames(expd_matrix),
labRow = rownames(expd_matrix),
heatmap_layers = theme(axis.line=element_blank())
)
p
# save the widget
# library(htmlwidgets)
# saveWidget(p, file= "~/.../heatmap.html")